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Physiofit update wrapper galaxy1 #317

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Physiofit update wrapper galaxy1 #317

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b0be288
Merge remote-tracking branch 'refs/remotes/origin/master'
llegregam Jun 26, 2024
07bee94
Merge branch 'workflow4metabolomics:master' into master
llegregam Jun 26, 2024
545be21
Merge branch 'workflow4metabolomics:master' into master
llegregam Dec 18, 2024
a7da4fa
Merge branch 'workflow4metabolomics:master' into master
llegregam Jan 22, 2025
74a3b18
Update_influx_si_data_manager v1.0.3
llegregam Jun 2, 2025
e3e3ad9
Added verbose option to wrapper
llegregam Jun 2, 2025
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10 changes: 6 additions & 4 deletions tools/influx_data_manager/influx_data_manager.xml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
<tool id="influx_data_manager" name="Influx Data Connector: Handling influx_si data inputs in Galaxy workflows" version="@TOOL_VERSION@+galaxy0" profile="23.0">
<tool id="influx_data_manager" name="Influx Data Connector: Handling influx_si data inputs in Galaxy workflows" version="@TOOL_VERSION@+galaxy1" profile="23.0">
<macros>
<token name='@TOOL_VERSION@'>1.0.2</token>
<token name='@TOOL_VERSION@'>1.0.3</token>
</macros>
<requirements>
<requirement type='package' version='@TOOL_VERSION@'>influx-si-data-manager</requirement>
Expand All @@ -9,6 +9,7 @@
influx_data_manager
--physiofit '$physiofit'
--isocor '$isocor'
--mapping '$mapping'
--linp '$linp'
--netw '$netw'
--mmet '$mmet'
Expand All @@ -28,12 +29,13 @@
<param type='data' format='tabular,txt' argument='--mmet' label='File containing specie concentrations for experiments (.mmet file)' optional='true'/>
<param type='data' format='tabular,txt' argument='--cnstr' label='File containing constraints onf fluxes and specie concentrations for experiments (.constr file)' optional='true'/>
<param type='data' format='tabular,txt' argument='--opt' label='File containing options for influx_si (.opt file)' optional='true'/>
<param type='data' format='tabular,txt' argument='--mapping' label='Mapping of names and corresponding new names for input files' optional='true'/>
<param name='verbose' type='boolean' truevalue='--verbose' falsevalue='' label='Debug mode' help='Select "Yes" to have debug logs be printed out'/>
</inputs>
<outputs>
<data format='txt' name='stdout' label='Run log'/>
<collection type='list' label='Influx_si input files' name='list_output'>
<discover_datasets pattern='__name_and_ext__' format='zip'/>
<discover_datasets pattern='(?P&lt;name&gt;.+\.[^.]+)$' format='zip'/>
</collection>
<data format='txt' name='stderr' label='Influx DM error log'/>
</outputs>
Expand Down Expand Up @@ -85,4 +87,4 @@
}
</citation>
</citations>
</tool>
</tool>
6 changes: 4 additions & 2 deletions tools/physiofit/physiofit.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id='physiofit' name='PhysioFit: extracellular flux calculation' version='@TOOL_VERSION@+galaxy0' python_template_version='3.5' profile='21.05'>
<tool id='physiofit' name='PhysioFit: extracellular flux calculation' version='@TOOL_VERSION@+galaxy1' python_template_version='3.5' profile='21.05'>
<description>PhysioFit is a scientific tool designed to quantify cell growth parameters and uptake and production fluxes</description>
<macros>
<token name='@TOOL_VERSION@'>3.4.0</token>
Expand All @@ -15,12 +15,14 @@
--data $datafile
-or '$recap'
-oz $zip
$verbose
2> $log
]]>
</command>
<inputs>
<param name='datafile' type='data' format='tabular, txt' multiple='true' label='Upload data file containing biomass and concentration values'/>
<param name='configfile' type='data' format='yaml' multiple='true' label='Upload yaml configuration file containing run parameters'/>
<param name='verbose' type='boolean' truevalue='--debug_mode' falsevalue='' label='Debug mode' help='Select "Yes" to have debug logs be printed out'/>
</inputs>
<outputs>
<data name='recap' label='Summary file' format='csv'/>
Expand Down Expand Up @@ -99,4 +101,4 @@
}
</citation>
</citations>
</tool>
</tool>
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